I like the AD because it makes his auto attacks stronger.
11.52 armor pen will give you an ~83% damage versus a typical level 1 ADC with base armor and 9 flat armor seals. Without the armor pen you will deal ~76% damage instead.
9 AD marks will give you 8.55 physical damage. Graves has 80% scaling on his Q (up to 144% at closer range) and he has 54 base attack damage.
I'll run the math for you, assuming AD quints:
w/ Armor Pen
60.75 AD at level 1, reduced to 83% damage
Graves deals 50.42 damage per auto attack
Min Buckshot deals 49.8 + 40.34 = 90.1 damage
Max buckshot deals 89.64 + 72.61 = 162.25 damage
w/ AD
69.3 AD at level 1, reduced to 76% damage
Graves deals 52.67 damage per auto attack
Min Buckshot deals 45.6 + 42.13 = 87.73
Max buckshot deals 82.08 + 75.84 = 157.92 damage
So as you can see, flat AD is better if you're auto attacking. Penetration is better if you're using abilities. The margin on either end is quite small. The difference is that AD makes CSing easier, and auto attacks don't cost mana or cooldowns. In the end the flat AD wins for these reasons IMO. The reason people take armor pen on a champion like Zed is because the majority of his damage and harass comes from his abilities in lane, unlike graves who will harass quite a bit with his auto attacks.